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Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Kalani L, Jorge-Torres OC, Esteller M, Ausio J, Abian O, Velazquez-Campoy A. Extending MeCP2 interactome: canonical nucleosomal histones interact with MeCP2. Nucleic Acids Res 2024; 52:3636-3653. [PMID: 38321951 DOI: 10.1093/nar/gkae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/08/2024] Open
Abstract
MeCP2 is a general regulator of transcription involved in the repression/activation of genes depending on the local epigenetic context. It acts as a chromatin regulator and binds with exquisite specificity to gene promoters. The set of epigenetic marks recognized by MeCP2 has been already established (mainly, cytosine modifications in CpG and CpA), as well as many of the constituents of its interactome. We unveil a new set of interactions for MeCP2 with the four canonical nucleosomal histones. MeCP2 interacts with high affinity with H2A, H2B, H3 and H4. In addition, Rett syndrome associated mutations in MeCP2 and histone epigenetic marks modulate these interactions. Given the abundance and the structural/functional relevance of histones and their involvement in epigenetic regulation, this new set of interactions and its modulating elements provide a new addition to the 'alphabet' for this epigenetic reader.
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Affiliation(s)
- David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | | | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Ladan Kalani
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BCV8W 2Y2, Canada
| | - Olga C Jorge-Torres
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08907 l'Hospitalet de Llobregat, Barcelona, Spain
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BCV8W 2Y2, Canada
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
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2
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Mehmood A, Shah S, Guo RY, Haider A, Shi M, Ali H, Ali I, Ullah R, Li B. Methyl-CpG-Binding Protein 2 Emerges as a Central Player in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorders. Cell Mol Neurobiol 2023; 43:4071-4101. [PMID: 37955798 DOI: 10.1007/s10571-023-01432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
MECP2 and its product methyl-CpG binding protein 2 (MeCP2) are associated with multiple sclerosis (MS) and neuromyelitis optica spectrum disorders (NMOSD), which are inflammatory, autoimmune, and demyelinating disorders of the central nervous system (CNS). However, the mechanisms and pathways regulated by MeCP2 in immune activation in favor of MS and NMOSD are not fully understood. We summarize findings that use the binding properties of MeCP2 to identify its targets, particularly the genes recognized by MeCP2 and associated with several neurological disorders. MeCP2 regulates gene expression in neurons, immune cells and during development by modulating various mechanisms and pathways. Dysregulation of the MeCP2 signaling pathway has been associated with several disorders, including neurological and autoimmune diseases. A thorough understanding of the molecular mechanisms underlying MeCP2 function can provide new therapeutic strategies for these conditions. The nervous system is the primary system affected in MeCP2-associated disorders, and other systems may also contribute to MeCP2 action through its target genes. MeCP2 signaling pathways provide promise as potential therapeutic targets in progressive MS and NMOSD. MeCP2 not only increases susceptibility and induces anti-inflammatory responses in immune sites but also leads to a chronic increase in pro-inflammatory cytokines gene expression (IFN-γ, TNF-α, and IL-1β) and downregulates the genes involved in immune regulation (IL-10, FoxP3, and CX3CR1). MeCP2 may modulate similar mechanisms in different pathologies and suggest that treatments for MS and NMOSD disorders may be effective in treating related disorders. MeCP2 regulates gene expression in MS and NMOSD. However, dysregulation of the MeCP2 signaling pathway is implicated in these disorders. MeCP2 plays a role as a therapeutic target for MS and NMOSD and provides pathways and mechanisms that are modulated by MeCP2 in the regulation of gene expression.
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Affiliation(s)
- Arshad Mehmood
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Suleman Shah
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Ruo-Yi Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Arsalan Haider
- Key Lab of Health Psychology, Institute of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Mengya Shi
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Hamid Ali
- Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, 44000, Pakistan
| | - Ijaz Ali
- Centre for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Hawally, 32093, Kuwait
| | - Riaz Ullah
- Medicinal Aromatic and Poisonous Plants Research Center, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Bin Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China.
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China.
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3
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Zhou J, Cattoglio C, Shao Y, Tirumala HP, Vetralla C, Bajikar SS, Li Y, Chen H, Wang Q, Wu Z, Tang B, Zahabiyon M, Bajic A, Meng X, Ferrie JJ, LaGrone A, Zhang P, Kim JJ, Tang J, Liu Z, Darzacq X, Heintz N, Tjian R, Zoghbi HY. A novel pathogenic mutation of MeCP2 impairs chromatin association independent of protein levels. Genes Dev 2023; 37:883-900. [PMID: 37890975 PMCID: PMC10691473 DOI: 10.1101/gad.350733.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023]
Abstract
Loss-of-function mutations in MECP2 cause Rett syndrome (RTT), a severe neurological disorder that mainly affects girls. Mutations in MECP2 do occur in males occasionally and typically cause severe encephalopathy and premature lethality. Recently, we identified a missense mutation (c.353G>A, p.Gly118Glu [G118E]), which has never been seen before in MECP2, in a young boy who suffered from progressive motor dysfunction and developmental delay. To determine whether this variant caused the clinical symptoms and study its functional consequences, we established two disease models, including human neurons from patient-derived iPSCs and a knock-in mouse line. G118E mutation partially reduces MeCP2 abundance and its DNA binding, and G118E mice manifest RTT-like symptoms seen in the patient, affirming the pathogenicity of this mutation. Using live-cell and single-molecule imaging, we found that G118E mutation alters MeCP2's chromatin interaction properties in live neurons independently of its effect on protein levels. Here we report the generation and characterization of RTT models of a male hypomorphic variant and reveal new insight into the mechanism by which this pathological mutation affects MeCP2's chromatin dynamics. Our ability to quantify protein dynamics in disease models lays the foundation for harnessing high-resolution single-molecule imaging as the next frontier for developing innovative therapies for RTT and other diseases.
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Affiliation(s)
- Jian Zhou
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Yingyao Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Harini P Tirumala
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Carlo Vetralla
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
- School of Medicine and Surgery, University of Milan-Bicocca, Milano 20126, Italy
| | - Sameer S Bajikar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Yan Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Hu Chen
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Qi Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhenyu Wu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bing Tang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mahla Zahabiyon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Aleksandar Bajic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Xiangling Meng
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jack J Ferrie
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Anel LaGrone
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ping Zhang
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jean J Kim
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jianrong Tang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
| | - Nathaniel Heintz
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA;
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
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4
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Oluigbo DC. Rett Syndrome: A Tale of Altered Genetics, Synaptic Plasticity, and Neurodevelopmental Dynamics. Cureus 2023; 15:e41555. [PMID: 37554594 PMCID: PMC10405636 DOI: 10.7759/cureus.41555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2023] [Indexed: 08/10/2023] Open
Abstract
Rett syndrome (RTT) is a neurodevelopmental disorder that is a leading cause of severe cognitive and physical impairment. RTT typically occurs in females, although rare cases of males with the disease exist. Its genetic cause, symptoms, and clinical progression timeline have also become well-documented since its initial discovery. However, a relatively late diagnosis and lack of an available cure signify that our understanding of the disease is incomplete. Innovative research methods and tools are thereby helping to fill gaps in our knowledge of RTT. Specifically, mouse models of RTT, video analysis, and retrospective parental analysis are well-established tools that provide valuable insights into RTT. Moreover, current and anticipated treatment options are improving the quality of life of the RTT patient population. Collectively, these developments are creating optimistic future perspectives for RTT.
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Affiliation(s)
- David C Oluigbo
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, USA
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5
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Chua GNL, Watters JW, Olinares PDB, Luo JA, Chait BT, Liu S. Differential dynamics specify MeCP2 function at methylated DNA and nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543478. [PMID: 37333354 PMCID: PMC10274721 DOI: 10.1101/2023.06.02.543478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Methyl-CpG-binding protein 2 (MeCP2) is an essential chromatin-binding protein whose mutations cause Rett syndrome (RTT), a leading cause of monogenic intellectual disabilities in females. Despite its significant biomedical relevance, the mechanism by which MeCP2 navigates the chromatin epigenetic landscape to regulate chromatin structure and gene expression remains unclear. Here, we used correlative single-molecule fluorescence and force microscopy to directly visualize the distribution and dynamics of MeCP2 on a variety of DNA and chromatin substrates. We found that MeCP2 exhibits differential diffusion dynamics when bound to unmethylated and methylated bare DNA. Moreover, we discovered that MeCP2 preferentially binds nucleosomes within the context of chromatinized DNA and stabilizes them from mechanical perturbation. The distinct behaviors of MeCP2 at bare DNA and nucleosomes also specify its ability to recruit TBLR1, a core component of the NCoR1/2 co-repressor complex. We further examined several RTT mutations and found that they disrupt different aspects of the MeCP2-chromatin interaction, rationalizing the heterogeneous nature of the disease. Our work reveals the biophysical basis for MeCP2's methylation-dependent activities and suggests a nucleosome-centric model for its genomic distribution and gene repressive functions. These insights provide a framework for delineating the multifaceted functions of MeCP2 and aid in our understanding of the molecular mechanisms of RTT.
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Affiliation(s)
- Gabriella N. L. Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - John W. Watters
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Paul Dominic B. Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua A. Luo
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
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6
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Li X, Nie Y, Qiu Z, Wang S. Human MECP2 transgenic rats show increased anxiety, severe social deficits, and abnormal prefrontal neural oscillation stability. Biochem Biophys Res Commun 2023; 648:28-35. [PMID: 36724557 DOI: 10.1016/j.bbrc.2023.01.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Methylated CpG binding protein 2 (MeCP2) plays an important role in the development and normal function of the neural system. Abnormally high expression of MECP2 leads to a subtype of autism called MECP2 duplication syndrome and MECP2 is considered one of the key pathogenic genes for autism spectrum disorders. However, the effect of MECP2 overexpression on neural activity is still not fully understood. Thus, transgenic (TG) animals that abnormally overexpress MeCP2 are important disease models in research on neurological function and autism. To create an animal model with a stronger and more stable autism phenotype, this study established a human MECP2 TG rat model and evaluated its movement ability, anxiety, and social behavior through behavioral tests. The results showed that MECP2 TG rats had an abnormally increased anxiety phenotype and social deficits in terms of abnormal social approach and social novelty preference, but no movement disorder. These autism-like behavioral phenotypes suggest that human MECP2 TG rats are suitable models for studying autism as they show more severe social deficit phenotypes and without interference from movement disorders affecting other phenotypes, which is an issue for mouse models with MECP2 duplication. In addition, this study performed preliminary exploration of the influence of the human MECP2 transgene on neural oscillation stability of the medial prefrontal cortex (mPFC), which is an important brain region for social interactions. Oscillation stability in MECP2 TG rats showed abnormal responses to social conditions. Overall, the results of this study provide a new research tool for understanding the mechanism of social impairment and treatment of autism. The results also provide evidence for the influence of MECP2 duplication on mPFC neural activity.
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Affiliation(s)
- Xiao Li
- Institute of Intelligent Robotics, Academy for Engineering and Technology, Fudan University, Shanghai, China; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Yingnan Nie
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Zilong Qiu
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
| | - Shouyan Wang
- Institute of Intelligent Robotics, Academy for Engineering and Technology, Fudan University, Shanghai, China; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
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7
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Farley SJ, Grishok A, Zeldich E. Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain. Epigenetics Chromatin 2022; 15:39. [PMID: 36463299 PMCID: PMC9719135 DOI: 10.1186/s13072-022-00471-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
Intellectual disability is a well-known hallmark of Down Syndrome (DS) that results from the triplication of the critical region of human chromosome 21 (HSA21). Major studies were conducted in recent years to gain an understanding about the contribution of individual triplicated genes to DS-related brain pathology. Global transcriptomic alterations and widespread changes in the establishment of neural lineages, as well as their differentiation and functional maturity, suggest genome-wide chromatin organization alterations in trisomy. High Mobility Group Nucleosome Binding Domain 1 (HMGN1), expressed from HSA21, is a chromatin remodeling protein that facilitates chromatin decompaction and is associated with acetylated lysine 27 on histone H3 (H3K27ac), a mark correlated with active transcription. Recent studies causatively linked overexpression of HMGN1 in trisomy and the development of DS-associated B cell acute lymphoblastic leukemia (B-ALL). HMGN1 has been shown to antagonize the activity of the Polycomb Repressive Complex 2 (PRC2) and prevent the deposition of histone H3 lysine 27 trimethylation mark (H3K27me3), which is associated with transcriptional repression and gene silencing. However, the possible ramifications of the increased levels of HMGN1 through the derepression of PRC2 target genes on brain cell pathology have not gained attention. In this review, we discuss the functional significance of HMGN1 in brain development and summarize accumulating reports about the essential role of PRC2 in the development of the neural system. Mechanistic understanding of how overexpression of HMGN1 may contribute to aberrant brain cell phenotypes in DS, such as altered proliferation of neural progenitors, abnormal cortical architecture, diminished myelination, neurodegeneration, and Alzheimer's disease-related pathology in trisomy 21, will facilitate the development of DS therapeutic approaches targeting chromatin.
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Affiliation(s)
- Sean J. Farley
- grid.189504.10000 0004 1936 7558Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Alla Grishok
- grid.189504.10000 0004 1936 7558Department of Biochemistry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA ,grid.189504.10000 0004 1936 7558Boston University Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Ella Zeldich
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
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8
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Mok RSF, Zhang W, Sheikh TI, Pradeepan K, Fernandes IR, DeJong LC, Benigno G, Hildebrandt MR, Mufteev M, Rodrigues DC, Wei W, Piekna A, Liu J, Muotri AR, Vincent JB, Muller L, Martinez-Trujillo J, Salter MW, Ellis J. Wide spectrum of neuronal and network phenotypes in human stem cell-derived excitatory neurons with Rett syndrome-associated MECP2 mutations. Transl Psychiatry 2022; 12:450. [PMID: 36253345 PMCID: PMC9576700 DOI: 10.1038/s41398-022-02216-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/19/2022] Open
Abstract
Rett syndrome (RTT) is a severe neurodevelopmental disorder primarily caused by heterozygous loss-of-function mutations in the X-linked gene MECP2 that is a global transcriptional regulator. Mutations in the methyl-CpG binding domain (MBD) of MECP2 disrupt its interaction with methylated DNA. Here, we investigate the effect of a novel MECP2 L124W missense mutation in the MBD of an atypical RTT patient with preserved speech in comparison to severe MECP2 null mutations. L124W protein had a limited ability to disrupt heterochromatic chromocenters due to decreased binding dynamics. We isolated two pairs of isogenic WT and L124W induced pluripotent stem cells. L124W induced excitatory neurons expressed stable protein, exhibited increased input resistance and decreased voltage-gated Na+ and K+ currents, and their neuronal dysmorphology was limited to decreased dendritic complexity. Three isogenic pairs of MECP2 null neurons had the expected more extreme morphological and electrophysiological phenotypes. We examined development and maturation of L124W and MECP2 null excitatory neural network activity using micro-electrode arrays. Relative to isogenic controls, L124W neurons had an increase in synchronous network burst frequency, in contrast to MECP2 null neurons that suffered a significant decrease in synchronous network burst frequency and a transient extension of network burst duration. A biologically motivated computational neural network model shows the observed changes in network dynamics are explained by changes in intrinsic Na+ and K+ currents in individual neurons. Our multilevel results demonstrate that RTT excitatory neurons show a wide spectrum of morphological, electrophysiological and circuitry phenotypes that are dependent on the severity of the MECP2 mutation.
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Grants
- R01 MH108528 NIMH NIH HHS
- MOP-133423 CIHR
- R01 MH109885 NIMH NIH HHS
- FDN-154336 CIHR
- R01 MH100175 NIMH NIH HHS
- Col Harland Sanders Rett Syndrome Research Fund at the University of Toronto (to J.E.), SFARI (Research grant #514918 to J.E. and J.M-T), CIHR (MOP-133423 to J.E. and M.W.S.; ERARE Team Grant ERT161303 to J.E.), CIHR foundation grant (FDN-154336 to M.W.S), Ontario Brain Institute (POND Network to J.E.), McLaughlin Centre Accelerator grant (to J.E.), John Evans Leadership Fund & Ontario Research Fund (to J.E), Canada Research Chair in Stem Cell Models of Childhood Disease (to J.E.), Beta Sigma Phi International Endowment Fund (to J.E.).
- BrainsCAN at Western University through the Canada First Research Excellence Fund (CFREF) (to GB, KP, LM, JMT). NSERC Postgraduate Scholarship–Doctoral (PGS-D) Scholarship to KP.
- Trainee support was provided by Restracomp (to LCD).
- National Institutes of Health (NIH) grants # R01MH108528, R01MH109885, and R01MH1000175 to ARM.
- Ontario Rett Syndrome Association to JBV.
- SFARI (Research grant #514918 to J.E. and J.M-T), BrainsCAN at Western University through the Canada First Research Excellence Fund (CFREF) (to GB, KP, LM, JMT)
- CIHR (MOP-133423 to J.E. and M.W.S.; CIHR foundation grant (FDN-154336 to M.W.S),
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Affiliation(s)
- Rebecca S F Mok
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wenbo Zhang
- Neurosciences & Mental Health Program, The Hospital for Sick Children, Toronto, M5G 0A4, ON, Canada
| | - Taimoor I Sheikh
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
| | - Kartik Pradeepan
- Department of Physiology and Pharmacology, Department of Psychiatry, Neuroscience Graduate Program, Robarts Research and Brain and Mind Institutes, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - Isabella R Fernandes
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Leah C DeJong
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Gabriel Benigno
- Department of Applied Mathematics, Robarts Research Institute, Brain and Mind Institute, Western University, London, ON, N6A 5B7, Canada
| | - Matthew R Hildebrandt
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Marat Mufteev
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Deivid C Rodrigues
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wei Wei
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alina Piekna
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Jiajie Liu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alysson R Muotri
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, Center for Academic Research and Training in Anthropogeny, Archealization Center, Kavli Institute, University of California San Diego, La Jolla, CA, 92037, USA
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
| | - Lyle Muller
- Department of Applied Mathematics, Robarts Research Institute, Brain and Mind Institute, Western University, London, ON, N6A 5B7, Canada
| | - Julio Martinez-Trujillo
- Department of Physiology and Pharmacology, Department of Psychiatry, Neuroscience Graduate Program, Robarts Research and Brain and Mind Institutes, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - Michael W Salter
- Neurosciences & Mental Health Program, The Hospital for Sick Children, Toronto, M5G 0A4, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
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9
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Martín MG, Dotti CG. Plasma membrane and brain dysfunction of the old: Do we age from our membranes? Front Cell Dev Biol 2022; 10:1031007. [PMID: 36274849 PMCID: PMC9582647 DOI: 10.3389/fcell.2022.1031007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
One of the characteristics of aging is a gradual hypo-responsiveness of cells to extrinsic stimuli, mainly evident in the pathways that are under hormone control, both in the brain and in peripheral tissues. Age-related resistance, i.e., reduced response of receptors to their ligands, has been shown to Insulin and also to leptin, thyroid hormones and glucocorticoids. In addition, lower activity has been reported in aging for ß-adrenergic receptors, adenosine A2B receptor, and several other G-protein-coupled receptors. One of the mechanisms proposed to explain the loss of sensitivity to hormones and neurotransmitters with age is the loss of receptors, which has been observed in several tissues. Another mechanism that is finding more and more experimental support is related to the changes that occur with age in the lipid composition of the neuronal plasma membrane, which are responsible for changes in the receptors’ coupling efficiency to ligands, signal attenuation and pathway desensitization. In fact, recent works have shown that altered membrane composition—as occurs during neuronal aging—underlies reduced response to glutamate, to the neurotrophin BDNF, and to insulin, all these leading to cognition decay and epigenetic alterations in the old. In this review we present evidence that altered functions of membrane receptors due to altered plasma membrane properties may be a triggering factor in physiological decline, decreased brain function, and increased vulnerability to neuropathology in aging.
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Affiliation(s)
- Mauricio G. Martín
- Cellular and Molecular Neurobiology Department, Instituto Ferreyra (INIMEC)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
- *Correspondence: Mauricio G. Martín, ; Carlos G. Dotti,
| | - Carlos G. Dotti
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- *Correspondence: Mauricio G. Martín, ; Carlos G. Dotti,
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10
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Schmidt A, Frei J, Poetsch A, Chittka A, Zhang H, Aßmann C, Lehmkuhl A, Bauer UM, Nuber UA, Cardoso MC. MeCP2 heterochromatin organization is modulated by arginine methylation and serine phosphorylation. Front Cell Dev Biol 2022; 10:941493. [PMID: 36172281 PMCID: PMC9510713 DOI: 10.3389/fcell.2022.941493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Rett syndrome is a human intellectual disability disorder that is associated with mutations in the X-linked MECP2 gene. The epigenetic reader MeCP2 binds to methylated cytosines on the DNA and regulates chromatin organization. We have shown previously that MECP2 Rett syndrome missense mutations are impaired in chromatin binding and heterochromatin reorganization. Here, we performed a proteomics analysis of post-translational modifications of MeCP2 isolated from adult mouse brain. We show that MeCP2 carries various post-translational modifications, among them phosphorylation on S80 and S421, which lead to minor changes in either heterochromatin binding kinetics or clustering. We found that MeCP2 is (di)methylated on several arginines and that this modification alters heterochromatin organization. Interestingly, we identified the Rett syndrome mutation site R106 as a dimethylation site. In addition, co-expression of protein arginine methyltransferases (PRMT)1 and PRMT6 lead to a decrease of heterochromatin clustering. Altogether, we identified and validated novel modifications of MeCP2 in the brain and show that these can modulate its ability to bind as well as reorganize heterochromatin, which may play a role in the pathology of Rett syndrome.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Jana Frei
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang, China
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Alexandra Chittka
- Division of Medicine, The Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Chris Aßmann
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Uta-Maria Bauer
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Ulrike A. Nuber
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
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11
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MeCP2 and transcriptional control of eukaryotic gene expression. Eur J Cell Biol 2022; 101:151237. [DOI: 10.1016/j.ejcb.2022.151237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/30/2022] [Accepted: 05/09/2022] [Indexed: 11/19/2022] Open
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12
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Zhang H, Romero H, Schmidt A, Gagova K, Qin W, Bertulat B, Lehmkuhl A, Milden M, Eck M, Meckel T, Leonhardt H, Cardoso MC. MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid–liquid phase separation and restricted by DNA methylation. Nucleus 2022; 13:1-34. [PMID: 35156529 PMCID: PMC8855868 DOI: 10.1080/19491034.2021.2024691] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Hui Zhang
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Hector Romero
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Annika Schmidt
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Katalina Gagova
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Faculty of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Bianca Bertulat
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Anne Lehmkuhl
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Manuela Milden
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Malte Eck
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Tobias Meckel
- Department of Chemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - M. Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
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13
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Brändle F, Frühbauer B, Jagannathan M. Principles and functions of pericentromeric satellite DNA clustering into chromocenters. Semin Cell Dev Biol 2022; 128:26-39. [PMID: 35144860 DOI: 10.1016/j.semcdb.2022.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022]
Abstract
Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.
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Affiliation(s)
- Franziska Brändle
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Benjamin Frühbauer
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Madhav Jagannathan
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland.
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14
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Collins BE, Neul JL. Rett Syndrome and MECP2 Duplication Syndrome: Disorders of MeCP2 Dosage. Neuropsychiatr Dis Treat 2022; 18:2813-2835. [PMID: 36471747 PMCID: PMC9719276 DOI: 10.2147/ndt.s371483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
Rett syndrome (RTT) is a neurodevelopmental disorder caused predominantly by loss-of-function mutations in the gene Methyl-CpG-binding protein 2 (MECP2), which encodes the MeCP2 protein. RTT is a MECP2-related disorder, along with MECP2 duplication syndrome (MDS), caused by gain-of-function duplications of MECP2. Nearly two decades of research have advanced our knowledge of MeCP2 function in health and disease. The following review will discuss MeCP2 protein function and its dysregulation in the MECP2-related disorders RTT and MDS. This will include a discussion of the genetic underpinnings of these disorders, specifically how sporadic X-chromosome mutations arise and manifest in specific populations. We will then review current diagnostic guidelines and clinical manifestations of RTT and MDS. Next, we will delve into MeCP2 biology, describing the dual landscapes of methylated DNA and its reader MeCP2 across the neuronal genome as well as the function of MeCP2 as a transcriptional modulator. Following this, we will outline common MECP2 mutations and genotype-phenotype correlations in both diseases, with particular focus on mutations associated with relatively mild disease in RTT. We will also summarize decades of disease modeling and resulting molecular, synaptic, and behavioral phenotypes associated with RTT and MDS. Finally, we list several therapeutics in the development pipeline for RTT and MDS and available evidence of their safety and efficacy.
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Affiliation(s)
- Bridget E Collins
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Jeffrey L Neul
- Vanderbilt Kennedy Center, Departments of Pediatrics, Pharmacology, and Special Education, Vanderbilt University Medical Center and Vanderbilt University, Nashville, TN, USA
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15
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Bouzroud W, Tazzite A, Berrada S, Gazzaz B, Dehbi H. R306X Mutation in the MECP2 Gene Causes an Atypical Rett Syndrome in a Moroccan Patient: A Case Report. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2022; 15:2632010X221124269. [PMID: 36147795 PMCID: PMC9486266 DOI: 10.1177/2632010x221124269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022]
Abstract
Rett syndrome (RTT) is a rare X-linked syndrome that predominantly affects girls.
It is characterized by a severe and progressive neurodevelopmental disorder with
neurological regression and autism spectrum features. The Rett syndrome is
associated with a broad phenotypic spectrum. It ranges from a classical Rett
syndrome defined by well-established criteria to atypical cases with symptoms
similar to other syndromes, such as Angelman syndrome. The first case of a
Moroccan female child carrying a R306X mutation in the MECP2
(Methyl-CpG-Binding Protein 2) gene, with an unusual manifestation of Rett
syndrome, is presented here. She showed autistic regression, behavioral
stagnation, epilepsy, unmotivated laughter, and craniofacial dysmorphia. Whole
exome sequencing revealed a nonsense mutation (R306X), resulting in a truncated,
nonfunctional MECP2 protein. The overlapping phenotypic spectrums between Rett
and Angelman syndromes have been described, and an interaction between the
MECP2 gene and the UBE3A (Ubiquitin
Protein Ligase E3A) gene pathways is possible but has not yet been proven. An
extensive genetic analysis is highly recommended in atypical cases to ensure an
accurate diagnosis and to improve patient management and genetic counseling.
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Affiliation(s)
- Wafaa Bouzroud
- Medical Genetics Laboratory, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Amal Tazzite
- Laboratory of Cellular and Molecular Pathology, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Sarah Berrada
- Medical Genetics Laboratory, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Bouchaïb Gazzaz
- Laboratory of Cellular and Molecular Pathology, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco.,Genetics Analysis Institute, Royal Gendarmerie, Rabat, Morocco
| | - Hind Dehbi
- Medical Genetics Laboratory, Ibn Rochd University Hospital, Casablanca, Morocco.,Laboratory of Cellular and Molecular Pathology, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
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16
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Neier K, Grant TE, Palmer RL, Chappell D, Hakam SM, Yasui KM, Rolston M, Settles ML, Hunter SS, Madany A, Ashwood P, Durbin-Johnson B, LaSalle JM, Yasui DH. Sex disparate gut microbiome and metabolome perturbations precede disease progression in a mouse model of Rett syndrome. Commun Biol 2021; 4:1408. [PMID: 34916612 PMCID: PMC8677842 DOI: 10.1038/s42003-021-02915-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/11/2021] [Indexed: 12/24/2022] Open
Abstract
Rett syndrome (RTT) is a regressive neurodevelopmental disorder in girls, characterized by multisystem complications including gut dysbiosis and altered metabolism. While RTT is known to be caused by mutations in the X-linked gene MECP2, the intermediate molecular pathways of progressive disease phenotypes are unknown. Mecp2 deficient rodents used to model RTT pathophysiology in most prior studies have been male. Thus, we utilized a patient-relevant mouse model of RTT to longitudinally profile the gut microbiome and metabolome across disease progression in both sexes. Fecal metabolites were altered in Mecp2e1 mutant females before onset of neuromotor phenotypes and correlated with lipid deficiencies in brain, results not observed in males. Females also displayed altered gut microbial communities and an inflammatory profile that were more consistent with RTT patients than males. These findings identify new molecular pathways of RTT disease progression and demonstrate the relevance of further study in female Mecp2 animal models.
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Affiliation(s)
- Kari Neier
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Tianna E Grant
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Rebecca L Palmer
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Demario Chappell
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Sophia M Hakam
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | | | - Matt Rolston
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | | | | | - Abdullah Madany
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Paul Ashwood
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Blythe Durbin-Johnson
- UC Davis Genome Center, Davis, CA, USA
- UC Davis School of Medicine, Department of Public Health Sciences, Davis, CA, USA
| | - Janine M LaSalle
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA.
- UC Davis Genome Center, Davis, CA, USA.
| | - Dag H Yasui
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
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17
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Zalosnik MI, Fabio MC, Bertoldi ML, Castañares CN, Degano AL. MeCP2 deficiency exacerbates the neuroinflammatory setting and autoreactive response during an autoimmune challenge. Sci Rep 2021; 11:10997. [PMID: 34040112 PMCID: PMC8155097 DOI: 10.1038/s41598-021-90517-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 05/12/2021] [Indexed: 02/04/2023] Open
Abstract
Rett syndrome is a severe and progressive neurological disorder linked to mutations in the MeCP2 gene. It has been suggested that immune alterations may play an active role in the generation and/or maintenance of RTT phenotypes. However, there is no clear consensus about which pathways are regulated in vivo by MeCP2 in the context of immune activation. In the present work we set to characterize the role of MeCP2 during the progression of Experimental Autoimmune Encephalomyelitis (EAE) using the MeCP2308/y mouse model (MUT), which represents a condition of "MeCP2 function deficiency". Our results showed that MeCP2 deficiency increased the susceptibility to develop EAE, along with a defective induction of anti-inflammatory responses and an exacerbated MOG-specific IFNγ expression in immune sites. In MUT-EAE spinal cord, we found a chronic increase in pro-inflammatory cytokines gene expression (IFNγ, TNFα and IL-1β) and downregulation of genes involved in immune regulation (IL-10, FoxP3 and CX3CR1). Moreover, our results indicate that MeCP2 acts intrinsically upon immune activation, affecting neuroimmune homeostasis by regulating the pro-inflammatory/anti-inflammatory balance in vivo. These results are relevant to identify the potential consequences of MeCP2 mutations on immune homeostasis and to explore novel therapeutic strategies for MeCP2-related disorders.
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Affiliation(s)
- M I Zalosnik
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CIQUIBIC, CONICET), Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina
| | - M C Fabio
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba (INIMEC-CONICET-UNC), Córdoba, Argentina
| | - M L Bertoldi
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CIQUIBIC, CONICET), Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina
| | - C N Castañares
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba (INIMEC-CONICET-UNC), Córdoba, Argentina
| | - A L Degano
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina.
- Centro de Investigaciones en Química Biológica de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CIQUIBIC, CONICET), Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina.
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18
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Sharifi O, Yasui DH. The Molecular Functions of MeCP2 in Rett Syndrome Pathology. Front Genet 2021; 12:624290. [PMID: 33968128 PMCID: PMC8102816 DOI: 10.3389/fgene.2021.624290] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
MeCP2 protein, encoded by the MECP2 gene, binds to DNA and affects transcription. Outside of this activity the true range of MeCP2 function is still not entirely clear. As MECP2 gene mutations cause the neurodevelopmental disorder Rett syndrome in 1 in 10,000 female births, much of what is known about the biologic function of MeCP2 comes from studying human cell culture models and rodent models with Mecp2 gene mutations. In this review, the full scope of MeCP2 research available in the NIH Pubmed (https://pubmed.ncbi.nlm.nih.gov/) data base to date is considered. While not all original research can be mentioned due to space limitations, the main aspects of MeCP2 and Rett syndrome research are discussed while highlighting the work of individual researchers and research groups. First, the primary functions of MeCP2 relevant to Rett syndrome are summarized and explored. Second, the conflicting evidence and controversies surrounding emerging aspects of MeCP2 biology are examined. Next, the most obvious gaps in MeCP2 research studies are noted. Finally, the most recent discoveries in MeCP2 and Rett syndrome research are explored with a focus on the potential and pitfalls of novel treatments and therapies.
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Affiliation(s)
- Osman Sharifi
- LaSalle Laboratory, Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, CA, United States
| | - Dag H Yasui
- LaSalle Laboratory, Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, CA, United States
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19
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Sun J, Yang J, Miao X, Loh HH, Pei D, Zheng H. Proteins in DNA methylation and their role in neural stem cell proliferation and differentiation. CELL REGENERATION (LONDON, ENGLAND) 2021; 10:7. [PMID: 33649938 PMCID: PMC7921253 DOI: 10.1186/s13619-020-00070-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/25/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND Epigenetic modifications, namely non-coding RNAs, DNA methylation, and histone modifications such as methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation play a significant role in brain development. DNA methyltransferases, methyl-CpG binding proteins, and ten-eleven translocation proteins facilitate the maintenance, interpretation, and removal of DNA methylation, respectively. Different forms of methylation, including 5-methylcytosine, 5-hydroxymethylcytosine, and other oxidized forms, have been detected by recently developed sequencing technologies. Emerging evidence suggests that the diversity of DNA methylation patterns in the brain plays a key role in fine-tuning and coordinating gene expression in the development, plasticity, and disorders of the mammalian central nervous system. Neural stem cells (NSCs), originating from the neuroepithelium, generate neurons and glial cells in the central nervous system and contribute to brain plasticity in the adult mammalian brain. MAIN BODY Here, we summarized recent research in proteins responsible for the establishment, maintenance, interpretation, and removal of DNA methylation and those involved in the regulation of the proliferation and differentiation of NSCs. In addition, we discussed the interactions of chemicals with epigenetic pathways to regulate NSCs as well as the connections between proteins involved in DNA methylation and human diseases. CONCLUSION Understanding the interplay between DNA methylation and NSCs in a broad biological context can facilitate the related studies and reduce potential misunderstanding.
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Affiliation(s)
- Jiaqi Sun
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China.
| | - Junzheng Yang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China
| | - Xiaoli Miao
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China
| | - Horace H Loh
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China
| | - Duanqing Pei
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China.,CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, 510530, China.,Institutes for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,School of Life Science, Westlake University, Hangzhou, 310024, China
| | - Hui Zheng
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China. .,CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, 510530, China. .,Institutes for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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Clinton SM, Shupe EA, Glover ME, Unroe KA, McCoy CR, Cohen JL, Kerman IA. Modeling heritability of temperamental differences, stress reactivity, and risk for anxiety and depression: Relevance to research domain criteria (RDoC). Eur J Neurosci 2021; 55:2076-2107. [PMID: 33629390 PMCID: PMC8382785 DOI: 10.1111/ejn.15158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/29/2021] [Accepted: 02/20/2021] [Indexed: 01/04/2023]
Abstract
Animal models provide important tools to study biological and environmental factors that shape brain function and behavior. These models can be effectively leveraged by drawing on concepts from the National Institute of Mental Health Research Domain Criteria (RDoC) Initiative, which aims to delineate molecular pathways and neural circuits that underpin behavioral anomalies that transcend psychiatric conditions. To study factors that contribute to individual differences in emotionality and stress reactivity, our laboratory utilized Sprague-Dawley rats that were selectively bred for differences in novelty exploration. Selective breeding for low versus high locomotor response to novelty produced rat lines that differ in behavioral domains relevant to anxiety and depression, particularly the RDoC Negative Valence domains, including acute threat, potential threat, and loss. Bred Low Novelty Responder (LR) rats, relative to their High Responder (HR) counterparts, display high levels of behavioral inhibition, conditioned and unconditioned fear, avoidance, passive stress coping, anhedonia, and psychomotor retardation. The HR/LR traits are heritable, emerge in the first weeks of life, and appear to be driven by alterations in the developing amygdala and hippocampus. Epigenomic and transcriptomic profiling in the developing and adult HR/LR brain suggest that DNA methylation and microRNAs, as well as differences in monoaminergic transmission (dopamine and serotonin in particular), contribute to their distinct behavioral phenotypes. This work exemplifies ways that animal models such as the HR/LR rats can be effectively used to study neural and molecular factors driving emotional behavior, which may pave the way toward improved understanding the neurobiological mechanisms involved in emotional disorders.
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Affiliation(s)
- Sarah M Clinton
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Elizabeth A Shupe
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Matthew E Glover
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Keaton A Unroe
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Chelsea R McCoy
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Joshua L Cohen
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
| | - Ilan A Kerman
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.,Behavioral Health Service Line, Veterans Affairs Pittsburgh Health System, Pittsburgh, PA, USA
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21
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Unraveling Molecular Pathways Altered in MeCP2-Related Syndromes, in the Search for New Potential Avenues for Therapy. Biomedicines 2021; 9:biomedicines9020148. [PMID: 33546327 PMCID: PMC7913493 DOI: 10.3390/biomedicines9020148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/25/2021] [Accepted: 01/30/2021] [Indexed: 12/27/2022] Open
Abstract
Methyl-CpG-binding protein 2 (MeCP2) is an X-linked epigenetic modulator whose dosage is critical for neural development and function. Loss-of-function mutations in MECP2 cause Rett Syndrome (RTT, OMIM #312750) while duplications in the Xq28 locus containing MECP2 and Interleukin-1 receptor-associated kinase 1 (IRAK1) cause MECP2 duplication syndrome (MDS, OMIM #300260). Both are rare neurodevelopmental disorders that share clinical symptoms, including intellectual disability, loss of speech, hand stereotypies, vasomotor deficits and seizures. The main objective of this exploratory study is to identify novel signaling pathways and potential quantitative biomarkers that could aid early diagnosis and/or the monitoring of disease progression in clinical trials. We analyzed by RT-PCR gene expression in whole blood and microRNA (miRNA) expression in plasma, in a cohort of 20 females with Rett syndrome, 2 males with MECP2 duplication syndrome and 28 healthy controls, and correlated RNA expression with disease and clinical parameters. We have identified a set of potential biomarker panels for RTT diagnostic and disease stratification of patients with microcephaly and vasomotor deficits. Our study sets the basis for larger studies leading to the identification of specific miRNA signatures for early RTT detection, stratification, disease progression and segregation from other neurodevelopmental disorders. Nevertheless, these data will require verification and validation in further studies with larger sample size including a whole range of ages.
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Role of DNA Methyl-CpG-Binding Protein MeCP2 in Rett Syndrome Pathobiology and Mechanism of Disease. Biomolecules 2021; 11:biom11010075. [PMID: 33429932 PMCID: PMC7827577 DOI: 10.3390/biom11010075] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/16/2022] Open
Abstract
Rett Syndrome (RTT) is a severe, rare, and progressive developmental disorder with patients displaying neurological regression and autism spectrum features. The affected individuals are primarily young females, and more than 95% of patients carry de novo mutation(s) in the Methyl-CpG-Binding Protein 2 (MECP2) gene. While the majority of RTT patients have MECP2 mutations (classical RTT), a small fraction of the patients (atypical RTT) may carry genetic mutations in other genes such as the cyclin-dependent kinase-like 5 (CDKL5) and FOXG1. Due to the neurological basis of RTT symptoms, MeCP2 function was originally studied in nerve cells (neurons). However, later research highlighted its importance in other cell types of the brain including glia. In this regard, scientists benefitted from modeling the disease using many different cellular systems and transgenic mice with loss- or gain-of-function mutations. Additionally, limited research in human postmortem brain tissues provided invaluable findings in RTT pathobiology and disease mechanism. MeCP2 expression in the brain is tightly regulated, and its altered expression leads to abnormal brain function, implicating MeCP2 in some cases of autism spectrum disorders. In certain disease conditions, MeCP2 homeostasis control is impaired, the regulation of which in rodents involves a regulatory microRNA (miR132) and brain-derived neurotrophic factor (BDNF). Here, we will provide an overview of recent advances in understanding the underlying mechanism of disease in RTT and the associated genetic mutations in the MECP2 gene along with the pathobiology of the disease, the role of the two most studied protein variants (MeCP2E1 and MeCP2E2 isoforms), and the regulatory mechanisms that control MeCP2 homeostasis network in the brain, including BDNF and miR132.
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MeCP2 links heterochromatin condensates and neurodevelopmental disease. Nature 2020; 586:440-444. [PMID: 32698189 DOI: 10.1038/s41586-020-2574-4] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 07/15/2020] [Indexed: 12/15/2022]
Abstract
Methyl CpG binding protein 2 (MeCP2) is a key component of constitutive heterochromatin, which is crucial for chromosome maintenance and transcriptional silencing1-3. Mutations in the MECP2 gene cause the progressive neurodevelopmental disorder Rett syndrome3-5, which is associated with severe mental disability and autism-like symptoms that affect girls during early childhood. Although previously thought to be a dense and relatively static structure1,2, heterochromatin is now understood to exhibit properties consistent with a liquid-like condensate6,7. Here we show that MeCP2 is a dynamic component of heterochromatin condensates in cells, and is stimulated by DNA to form liquid-like condensates. MeCP2 contains several domains that contribute to the formation of condensates, and mutations in MECP2 that lead to Rett syndrome disrupt the ability of MeCP2 to form condensates. Condensates formed by MeCP2 selectively incorporate and concentrate heterochromatin cofactors rather than components of euchromatic transcriptionally active condensates. We propose that MeCP2 enhances the separation of heterochromatin and euchromatin through its condensate partitioning properties, and that disruption of condensates may be a common consequence of mutations in MeCP2 that cause Rett syndrome.
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Epigenetic Factors That Control Pericentric Heterochromatin Organization in Mammals. Genes (Basel) 2020; 11:genes11060595. [PMID: 32481609 PMCID: PMC7349813 DOI: 10.3390/genes11060595] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Pericentric heterochromatin (PCH) is a particular form of constitutive heterochromatin that is localized to both sides of centromeres and that forms silent compartments enriched in repressive marks. These genomic regions contain species-specific repetitive satellite DNA that differs in terms of nucleotide sequences and repeat lengths. In spite of this sequence diversity, PCH is involved in many biological phenomena that are conserved among species, including centromere function, the preservation of genome integrity, the suppression of spurious recombination during meiosis, and the organization of genomic silent compartments in the nucleus. PCH organization and maintenance of its repressive state is tightly regulated by a plethora of factors, including enzymes (e.g., DNA methyltransferases, histone deacetylases, and histone methyltransferases), DNA and histone methylation binding factors (e.g., MECP2 and HP1), chromatin remodeling proteins (e.g., ATRX and DAXX), and non-coding RNAs. This evidence helps us to understand how PCH organization is crucial for genome integrity. It then follows that alterations to the molecular signature of PCH might contribute to the onset of many genetic pathologies and to cancer progression. Here, we describe the most recent updates on the molecular mechanisms known to underlie PCH organization and function.
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25
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MeCP2 and Chromatin Compartmentalization. Cells 2020; 9:cells9040878. [PMID: 32260176 PMCID: PMC7226738 DOI: 10.3390/cells9040878] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/24/2022] Open
Abstract
Methyl-CpG binding protein 2 (MeCP2) is a multifunctional epigenetic reader playing a role in transcriptional regulation and chromatin structure, which was linked to Rett syndrome in humans. Here, we focus on its isoforms and functional domains, interactions, modifications and mutations found in Rett patients. Finally, we address how these properties regulate and mediate the ability of MeCP2 to orchestrate chromatin compartmentalization and higher order genome architecture.
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DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices. Epigenetics Chromatin 2020; 13:18. [PMID: 32178718 PMCID: PMC7076939 DOI: 10.1186/s13072-020-00339-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/06/2020] [Indexed: 11/29/2022] Open
Abstract
Background MeCP2 and MBD2 are members of a family of proteins that possess a domain that selectively binds 5-methylcytosine in a CpG context. Members of the family interact with other proteins to modulate DNA packing. Stretching of DNA–protein complexes in nanofluidic channels with a cross-section of a few persistence lengths allows us to probe the degree of compaction by proteins. Results We demonstrate DNA compaction by MeCP2 while MBD2 does not affect DNA configuration. By using atomic force microscopy (AFM), we determined that the mechanism for compaction by MeCP2 is the formation of bridges between distant DNA stretches and the formation of loops. Conclusions Despite sharing a similar specific DNA-binding domain, the impact of full-length 5-methylcytosine-binding proteins can vary drastically between strong compaction of DNA and no discernable large-scale impact of protein binding. We demonstrate that ATTO 565-labeled MBD2 is a good candidate as a staining agent for epigenetic mapping.
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Tillotson R, Bird A. The Molecular Basis of MeCP2 Function in the Brain. J Mol Biol 2020; 432:1602-1623. [PMID: 31629770 DOI: 10.1016/j.jmb.2019.10.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 12/14/2022]
Abstract
MeCP2 is a reader of the DNA methylome that occupies a large proportion of the genome due to its high abundance and the frequency of its target sites. It has been the subject of extensive study because of its link with 'MECP2-related disorders', of which Rett syndrome is the most prevalent. This review integrates evidence from patient mutation data with results of experimental studies using mouse models, cell lines and in vitro systems to critically evaluate our understanding of MeCP2 protein function. Recent evidence challenges the idea that MeCP2 is a multifunctional hub that integrates diverse processes to underpin neuronal function, suggesting instead that its primary role is to recruit the NCoR1/2 co-repressor complex to methylated sites in the genome, leading to dampening of gene expression.
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Affiliation(s)
- Rebekah Tillotson
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
| | - Adrian Bird
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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28
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Rett syndrome-causing mutations compromise MeCP2-mediated liquid-liquid phase separation of chromatin. Cell Res 2020; 30:393-407. [PMID: 32111972 DOI: 10.1038/s41422-020-0288-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
Rett syndrome (RTT), a severe postnatal neurodevelopmental disorder, is caused by mutations in the X-linked gene encoding methyl-CpG-binding protein 2 (MeCP2). MeCP2 is a chromatin organizer regulating gene expression. RTT-causing mutations have been shown to affect this function. However, the mechanism by which MeCP2 organizes chromatin is unclear. In this study, we found that MeCP2 can induce compaction and liquid-liquid phase separation of nucleosomal arrays in vitro, and DNA methylation further enhances formation of chromatin condensates by MeCP2. Interestingly, RTT-causing mutations compromise MeCP2-mediated chromatin phase separation, while benign variants have little effect on this process. Moreover, MeCP2 competes with linker histone H1 to form mutually exclusive chromatin condensates in vitro and distinct heterochromatin foci in vivo. RTT-causing mutations reduce or even abolish the ability of MeCP2 to compete with histone H1 and to form chromatin condensates. Together, our results identify a novel mechanism by which phase separation underlies MeCP2-mediated heterochromatin formation and reveal the potential link between this process and the pathology of RTT.
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Moran-Salvador E, Garcia-Macia M, Sivaharan A, Sabater L, Zaki MY, Oakley F, Knox A, Page A, Luli S, Mann J, Mann DA. Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells. Gastroenterology 2019; 157:1398-1412.e9. [PMID: 31352003 PMCID: PMC6853276 DOI: 10.1053/j.gastro.2019.07.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 07/12/2019] [Accepted: 07/17/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Methyl-CpG binding protein 2, MECP2, which binds to methylated regions of DNA to regulate transcription, is expressed by hepatic stellate cells (HSCs) and is required for development of liver fibrosis in mice. We investigated the effects of MECP2 deletion from HSCs on their transcriptome and of phosphorylation of MECP2 on HSC phenotype and liver fibrosis. METHODS We isolated HSCs from Mecp2-/y mice and wild-type (control) mice. HSCs were activated in culture and used in array analyses of messenger RNAs and long noncoding RNAs. Kyoto Encyclopedia of Genes and Genomes pathway analyses identified pathways regulated by MECP2. We studied mice that expressed a mutated form of Mecp2 that encodes the S80A substitution, MECP2S80, causing loss of MECP2 phosphorylation at serine 80. Liver fibrosis was induced in these mice by administration of carbon tetrachloride, and liver tissues and HSCs were collected and analyzed. RESULTS MECP2 deletion altered expression of 284 messenger RNAs and 244 long noncoding RNAs, including those that regulate DNA replication; are members of the minichromosome maintenance protein complex family; or encode CDC7, HAS2, DNA2 (a DNA helicase), or RPA2 (a protein that binds single-stranded DNA). We found that MECP2 regulates the DNA repair Fanconi anemia pathway in HSCs. Phosphorylation of MECP2S80 and its putative kinase, HAS2, were induced during transdifferentiation of HSCs. HSCs from MECP2S80 mice had reduced proliferation, and livers from these mice had reduced fibrosis after carbon tetrachloride administration. CONCLUSIONS In studies of mice with disruption of Mecp2 or that expressed a form of MECP2 that is not phosphorylated at S80, we found phosphorylation of MECP2 to be required for HSC proliferation and induction of fibrosis. In HSCs, MECP2 regulates expression of genes required for DNA replication and repair. Strategies to inhibit MECP2 phosphorylation at S80 might be developed for treatment of liver fibrosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jelena Mann
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
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Genomic insights into MeCP2 function: A role for the maintenance of chromatin architecture. Curr Opin Neurobiol 2019; 59:174-179. [PMID: 31430649 DOI: 10.1016/j.conb.2019.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/07/2019] [Indexed: 01/05/2023]
Abstract
Methyl-CpG binding protein 2 (MeCP2) plays fundamental roles in the nervous system, as both gain-of-function and loss-of-function of MECP2 are associated with severe neurological conditions. Understanding the molecular function of MeCP2 will not only provide insights into the pathogenesis of MeCP2-related disorders, but will also shed light on the epigenetic regulation of neuronal function. In the past few years, a number of studies have provided mechanistic evidence that MeCP2 recruits co-repressor complexes to particular sequences of methylated DNA. Additionally, innovative design and high-throughput sequencing technologies have provided opportunities to study the effects of MeCP2 on the neuronal transcriptome at an unprecedented level of detail, demonstrating that MeCP2 modulates gene expression in a context-specific manner. These findings have raised new questions and challenged current models of MeCP2 function. In this review, we describe several recent developments, highlight future challenges, and articulate a model by which MeCP2 functions as an organizer of chromatin architecture to modulate global gene expression in the nervous system.
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Keidar L, Gerlitz G, Kshirsagar A, Tsoory M, Olender T, Wang X, Yang Y, Chen YS, Yang YG, Voineagu I, Reiner O. Interplay of LIS1 and MeCP2: Interactions and Implications With the Neurodevelopmental Disorders Lissencephaly and Rett Syndrome. Front Cell Neurosci 2019; 13:370. [PMID: 31474834 PMCID: PMC6703185 DOI: 10.3389/fncel.2019.00370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
LIS1 is the main causative gene for lissencephaly, while MeCP2 is the main causative gene for Rett syndrome, both of which are neurodevelopmental diseases. Here we report nuclear functions for LIS1 and identify previously unrecognized physical and genetic interactions between the products of these two genes in the cell nucleus, that has implications on MeCP2 organization, neuronal gene expression and mouse behavior. Reduced LIS1 levels affect the association of MeCP2 with chromatin. Transcriptome analysis of primary cortical neurons derived from wild type, Lis1±, MeCP2−/y, or double mutants mice revealed a large overlap in the differentially expressed (DE) genes between the various mutants. Overall, our findings provide insights on molecular mechanisms involved in the neurodevelopmental disorders lissencephaly and Rett syndrome caused by dysfunction of LIS1 and MeCP2, respectively.
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Affiliation(s)
- Liraz Keidar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gabi Gerlitz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aditya Kshirsagar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Tsoory
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Xing Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ying Yang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yu-Sheng Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yun-Gui Yang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Abstract
Elucidating the functions of a particular gene is paramount to the understanding of how its dysfunction contributes to disease. This is especially important when the gene is implicated in multiple different disorders. One such gene is methyl-CpG-binding protein 2 (MECP2), which has been most prominently associated with the neurodevelopmental disorder Rett syndrome, as well as major neuropsychiatric disorders such as autism and schizophrenia. Being initially identified as a transcriptional regulator that modulates gene expression and subsequently also shown to be involved in other molecular events, dysfunction of the MeCP2 protein has the potential to affect many cellular processes. In this chapter, we will briefly review the functions of the MeCP2 protein and how its mutations are implicated in Rett syndrome and other neuropsychiatric disorders. We will further discuss about the mouse models that have been generated to specifically dissect the function of MeCP2 in different cell types and brain regions. It is envisioned that such thorough and targeted examination of MeCP2 functions can aid in enlightening the role that it plays in normal and dysfunctional physiological systems.
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Affiliation(s)
- Eunice W M Chin
- Neuroscience and Mental Health Faculty, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Eyleen L K Goh
- Neuroscience and Mental Health Faculty, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- Department of Research, National Neuroscience Institute, Singapore, Singapore.
- Neuroscience Academic Clinical Programme, Singhealth Duke-NUS Academic Medical Center, Singapore, Singapore.
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Marshall KL, Wang J, Ji T, Rivera RM. The effects of biological aging on global DNA methylation, histone modification, and epigenetic modifiers in the mouse germinal vesicle stage oocyte. Anim Reprod 2018; 15:1253-1267. [PMID: 34221140 PMCID: PMC8203117 DOI: 10.21451/1984-3143-ar2018-0087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A cultural trend in developed countries is favoring a delay in maternal age at first childbirth.
In mammals fertility and chronological age show an inverse correlation. Oocyte quality is
a contributing factor to this multifactorial phenomenon that may be influenced by age-related
changes in the oocyte epigenome. Based on previous reports, we hypothesized that advanced
maternal age would lead to alterations in the oocyte’s epigenome. We tested our hypothesis
by determining protein levels of various epigenetic modifications and modifiers in fully-grown
(≥70 µm), germinal vesicle (GV) stage oocytes of young (10-13 weeks) and aged
(69-70 weeks) mice. Our results demonstrate a significant increase in protein amounts of
the maintenance DNA methyltransferase DNMT1 (P = 0.003) and a trend toward increased global
DNA methylation (P = 0.09) with advanced age. MeCP2, a methyl DNA binding domain protein, recognizes
methylated DNA and induces chromatin compaction and silencing. We hypothesized that chromatin
associated MeCP2 would be increased similarly to DNA methylation in oocytes of aged female
mice. However, we detected a significant decrease (P = 0.0013) in protein abundance of MeCP2
between GV stage oocytes from young and aged females. Histone posttranslational modifications
can also alter chromatin conformation. Di-methylation of H3K9 (H3K9me2) is associated with
permissive heterochromatin while acetylation of H4K5 (H4K5ac) is associated with euchromatin.
Our results indicate a trend toward decreasing H3K9me2 (P = 0.077) with advanced female age
and no significant differences in levels of H4K5ac. These data demonstrate that physiologic
aging affects the mouse oocyte epigenome and provide a better understanding of the mechanisms
underlying the decrease in oocyte quality and reproductive potential of aged females.
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Affiliation(s)
- Kira Lynn Marshall
- Division of Animal Sciences.,Reproductive Sciences, San Diego Zoo Global Institute for Conservation Research, San Pasqual Valley Rd
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Dissection of structural dynamics of chromatin fibers by single-molecule magnetic tweezers. BIOPHYSICS REPORTS 2018; 4:222-232. [PMID: 30310859 PMCID: PMC6153500 DOI: 10.1007/s41048-018-0064-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/18/2018] [Indexed: 12/01/2022] Open
Abstract
The accessibility of genomic DNA, as a key determinant of gene-related processes, is dependent on the packing density and structural dynamics of chromatin fiber. However, due to the highly dynamic and heterogeneous properties of chromatin fiber, it is technically challenging to study these properties of chromatin. Here, we report a strategy for dissecting the dynamics of chromatin fibers based on single-molecule magnetic tweezers. Using magnetic tweezers, we can manipulate the chromatin fiber and trace its extension during the folding and unfolding process under tension to investigate the dynamic structural transitions at single-molecule level. The highly accurate and reliable in vitro single-molecule strategy provides a new research platform to dissect the structural dynamics of chromatin fiber and its regulation by different epigenetic factors during gene expression.
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Sharma K, Singh J, Pillai PP. MeCP2 Differentially Regulate the Myelin MBP and PLP Protein Expression in Oligodendrocytes and C6 Glioma. J Mol Neurosci 2018; 65:343-350. [DOI: 10.1007/s12031-018-1112-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022]
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36
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Limouse C, Bell JC, Fuller CJ, Straight AF, Mabuchi H. Measurement of Mesoscale Conformational Dynamics of Freely Diffusing Molecules with Tracking FCS. Biophys J 2018; 114:1539-1550. [PMID: 29642025 PMCID: PMC5954409 DOI: 10.1016/j.bpj.2018.01.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/27/2017] [Accepted: 01/02/2018] [Indexed: 11/19/2022] Open
Abstract
Few techniques are suited to probe the structure and dynamics of molecular complexes at the mesoscale level (∼100-1000 nm). We have developed a single-molecule technique that uses tracking fluorescence correlation spectroscopy (tFCS) to probe the conformation and dynamics of mesoscale molecular assemblies. tFCS measures the distance fluctuations between two fluorescently labeled sites within an untethered, freely diffusing biomolecule. To achieve subdiffraction spatial resolution, we developed a feedback scheme that allows us to maintain the molecule at an optimal position within the laser intensity gradient for fluorescence correlation spectroscopy. We characterized tFCS spatial sensitivity by measuring the Brownian end-to-end dynamics of DNA molecules as short as 1000 bp. We demonstrate that tFCS detects changes in the compaction of reconstituted nucleosome arrays and can assay transient protein-mediated interactions between distant sites in an individual DNA molecule. Our measurements highlight the applicability of tFCS to a wide variety of biochemical processes involving mesoscale conformational dynamics.
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Affiliation(s)
| | - Jason C Bell
- Department of Biochemistry, Stanford University, Stanford, California
| | - Colin J Fuller
- Department of Biochemistry, Stanford University, Stanford, California
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, California.
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Sheikh TI, Harripaul R, Ayub M, Vincent JB. MeCP2 AT-Hook1 mutations in patients with intellectual disability and/or schizophrenia disrupt DNA binding and chromatin compaction in vitro. Hum Mutat 2018; 39:717-728. [DOI: 10.1002/humu.23409] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/10/2018] [Accepted: 02/07/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Taimoor I. Sheikh
- Molecular Neuropsychiatry & Development (MiND) Lab; Campbell Family Mental Health Research Institute; Centre for Addiction and Mental Health; Toronto Ontario Canada
- Institute of Medical Science; University of Toronto; Toronto Ontario Canada
| | - Ricardo Harripaul
- Molecular Neuropsychiatry & Development (MiND) Lab; Campbell Family Mental Health Research Institute; Centre for Addiction and Mental Health; Toronto Ontario Canada
- Institute of Medical Science; University of Toronto; Toronto Ontario Canada
| | - Muhammad Ayub
- Lahore Institute of Research & Development; Lahore Pakistan
- Department of Psychiatry; Queen's University; Kingston Ontario Canada
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab; Campbell Family Mental Health Research Institute; Centre for Addiction and Mental Health; Toronto Ontario Canada
- Institute of Medical Science; University of Toronto; Toronto Ontario Canada
- Department of Psychiatry; University of Toronto; Toronto Ontario Canada
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38
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D'Annessa I, Gandaglia A, Brivio E, Stefanelli G, Frasca A, Landsberger N, Di Marino D. Tyr120Asp mutation alters domain flexibility and dynamics of MeCP2 DNA binding domain leading to impaired DNA interaction: Atomistic characterization of a Rett syndrome causing mutation. Biochim Biophys Acta Gen Subj 2018; 1862:1180-1189. [PMID: 29428602 DOI: 10.1016/j.bbagen.2018.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 11/28/2022]
Abstract
Mutations in the X-linked MECP2 gene represent the main origin of Rett syndrome, causing a profound intellectual disability in females. MeCP2 is an epigenetic transcriptional regulator containing two main functional domains: a methyl-CpG binding domain (MBD) and a transcription repression domain (TRD). Over 600 pathogenic mutations were reported to affect the whole protein; almost half of missense mutations affect the MBD. Understanding the impact of these mutations on the MBD structure and interaction with DNA will foster the comprehension of their pathogenicity and possibly genotype/phenotype correlation studies. Herein, we use molecular dynamics simulations to obtain a detailed view of the dynamics of WT and mutated MBD in the presence and absence of DNA. The pathogenic mutation Y120D is used as paradigm for our studies. Further, since the Y120 residue was previously found to be a phosphorylation site, we characterize the dynamic profile of the MBD also in the presence of Y120 phosphorylation (pY120). We found that addition of a phosphate group to Y120 or mutation in aspartic acid affect domain mobility that samples an alternative conformational space with respect to the WT, leading to impaired ability to interact with DNA. Experimental assays showing a significant reduction in the binding affinity between the mutated MBD and the DNA confirmed our predictions.
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Affiliation(s)
- Ilda D'Annessa
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milan, Italy
| | - Anna Gandaglia
- San Raffaele Rett Research Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Elena Brivio
- San Raffaele Rett Research Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Gilda Stefanelli
- San Raffaele Rett Research Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Angelisa Frasca
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Nicoletta Landsberger
- San Raffaele Rett Research Unit, San Raffaele Scientific Institute, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy.
| | - Daniele Di Marino
- Department of Informatics, Institute of Computational Science, Università della Svizzera Italiana, Lugano, Switzerland.
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Kyle SM, Vashi N, Justice MJ. Rett syndrome: a neurological disorder with metabolic components. Open Biol 2018; 8:170216. [PMID: 29445033 PMCID: PMC5830535 DOI: 10.1098/rsob.170216] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/18/2018] [Indexed: 02/06/2023] Open
Abstract
Rett syndrome (RTT) is a neurological disorder caused by mutations in the X-linked gene methyl-CpG-binding protein 2 (MECP2), a ubiquitously expressed transcriptional regulator. Despite remarkable scientific progress since its discovery, the mechanism by which MECP2 mutations cause RTT symptoms is largely unknown. Consequently, treatment options for patients are currently limited and centred on symptom relief. Thought to be an entirely neurological disorder, RTT research has focused on the role of MECP2 in the central nervous system. However, the variety of phenotypes identified in Mecp2 mutant mouse models and RTT patients implicate important roles for MeCP2 in peripheral systems. Here, we review the history of RTT, highlighting breakthroughs in the field that have led us to present day. We explore the current evidence supporting metabolic dysfunction as a component of RTT, presenting recent studies that have revealed perturbed lipid metabolism in the brain and peripheral tissues of mouse models and patients. Such findings may have an impact on the quality of life of RTT patients as both dietary and drug intervention can alter lipid metabolism. Ultimately, we conclude that a thorough knowledge of MeCP2's varied functional targets in the brain and body will be required to treat this complex syndrome.
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Affiliation(s)
- Stephanie M Kyle
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada M5G 0A4
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neeti Vashi
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada M5G 0A4
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A1
| | - Monica J Justice
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada M5G 0A4
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A1
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40
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Mushtaq AU, Lee Y, Hwang E, Bang JK, Hong E, Byun Y, Song JJ, Jeon YH. Biophysical characterization of the basic cluster in the transcription repression domain of human MeCP2 with AT-rich DNA. Biochem Biophys Res Commun 2018; 495:145-150. [DOI: 10.1016/j.bbrc.2017.10.169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
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41
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Zhang T, Meng J, Liu X, Zhang X, Peng X, Cheng Z, Zhang F. ING5 differentially regulates protein lysine acetylation and promotes p300 autoacetylation. Oncotarget 2017; 9:1617-1629. [PMID: 29416718 PMCID: PMC5788586 DOI: 10.18632/oncotarget.22176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 10/11/2017] [Indexed: 02/06/2023] Open
Abstract
ING5 belongs to the Inhibitor of Growth (ING) candidate tumor suppressor family. Previously, we have shown that ING5 inhibits invasiveness of lung cancer cells by downregulating EMT-inducing genes. However, the underlying mechanisms remain unclear. The aim of the study was to use integrated approach involving SILAC labeling and mass spectrometry-based quantitative proteomics to quantify dynamic changes of acetylation regulated by ING5 in lung cancer cells. Here, we have found that ING5 has a profound influence on protein lysine acetylation with 163 acetylation peptides on 122 proteins significantly upregulated and 100 acetylation peptides on 72 proteins downregulated by ING5 overexpression. Bioinfomatic analysis revealed that the acetylated proteins upregulated by ING5 located preferentially in nucleus to cytoplasm and were significantly enriched in transcription cofactor activity, chromatin binding and DNA binding functions; while those downregulated by ING5 located preferentially in cytoplasm rather than nucleus and were functionally enriched in metabolism, suggesting diverse functions of ING5 through differentially regulating protein acetylation. Interestingly, we found ING5 overexpression promotes p300 autoacetylation at K1555, K1558 and K1560 within p300 HAT domain, and two novel sites K1647 and K1794, leading to activation of p300 HAT activity, which was confirmed by accelerated acetylation of p300 target proteins, p53 at k382 and histone H3 at K18. A specific p300 HAT inhibitor C646 impaired ING5-increased acetylation of H3K18 and p53K382, and subsequent expression of p21 and Bax. In conclusion, our results reveal the lysine acetylome regulated by ING5 and provide new insights into mechanisms of ING5 in the regulation of gene expression, metabolism and other cellular functions.
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Affiliation(s)
- Tao Zhang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Jin Meng
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China.,Department of Pharmacy, No. 309 Hospital of PLA, Beijing 100091, China
| | - Xinli Liu
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Xutao Zhang
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Zhongyi Cheng
- Department of Bioinformatics, Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Feng Zhang
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
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Abstract
This paper provides a brief introductory review of the most recent advances in our knowledge about the structural and functional aspects of two transcriptional regulators: MeCP2, a protein whose mutated forms are involved in Rett syndrome; and CTCF, a constitutive transcriptional insulator. This is followed by a description of the PTMs affecting these two proteins and an analysis of their known interacting partners. A special emphasis is placed on the recent studies connecting these two proteins, focusing on the still poorly understood potential structural and functional interactions between the two of them on the chromatin substrate. An overview is provided for some of the currently known genes that are dually regulated by these two proteins. Finally, a model is put forward to account for their possible involvement in their regulation of gene expression.
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Affiliation(s)
- Juan Ausió
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,b Center for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Philippe T Georgel
- c Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA.,d Cell Differentiation and Development Center, Marshall University, Huntington, WV 25755, USA
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43
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Mendonca A, Sanchez OF, Liu W, Li Z, Yuan C. CpG dinucleotide positioning patterns determine the binding affinity of methyl-binding domain to nucleosomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:713-720. [DOI: 10.1016/j.bbagrm.2017.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/10/2017] [Accepted: 03/30/2017] [Indexed: 11/28/2022]
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44
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Pandey S, Pruitt K. Functional assessment of MeCP2 in Rett syndrome and cancers of breast, colon, and prostate. Biochem Cell Biol 2017; 95:368-378. [DOI: 10.1139/bcb-2016-0154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Ever since the first report that mutations in methyl-CpG-binding protein 2 (MeCP2) causes Rett syndrome (RTT), a severe neurological disorder in females world-wide, there has been a keen interest to gain a comprehensive understanding of this protein. While the classical model associated with MeCP2 function suggests its role in gene suppression via recruitment of co-repressor complexes and histone deacetylases to methylated CpG-sites, recent discoveries have brought to light its role in transcription activation, modulation of RNA splicing, and chromatin compaction. Various post-translational modifications (PTMs) of MeCP2 further increase its functional versatility. Involvement of MeCP2 in pathologies other than RTT, such as tumorigenesis however, remains poorly explored and understood. This review provides a survey of the literature implicating MeCP2 in breast, colon and prostate cancer.
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Affiliation(s)
- Somnath Pandey
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
| | - Kevin Pruitt
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
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45
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Transient receptor potential canonical type 3 channels: Interactions, role and relevance - A vascular focus. Pharmacol Ther 2017; 174:79-96. [DOI: 10.1016/j.pharmthera.2017.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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The Crucial Role of DNA Methylation and MeCP2 in Neuronal Function. Genes (Basel) 2017; 8:genes8050141. [PMID: 28505093 PMCID: PMC5448015 DOI: 10.3390/genes8050141] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/25/2017] [Accepted: 05/05/2017] [Indexed: 12/16/2022] Open
Abstract
A neuron is unique in its ability to dynamically modify its transcriptional output in response to synaptic activity while maintaining a core gene expression program that preserves cellular identity throughout a lifetime that is longer than almost every other cell type in the body. A contributing factor to the immense adaptability of a neuron is its unique epigenetic landscape that elicits locus-specific alterations in chromatin architecture, which in turn influences gene expression. One such epigenetic modification that is sensitive to changes in synaptic activity, as well as essential for maintaining cellular identity, is DNA methylation. The focus of this article is on the importance of DNA methylation in neuronal function, summarizing recent studies on critical players in the establishment of (the “writing”), the modification or erasure of (the “editing”), and the mediation of (the “reading”) DNA methylation in neurodevelopment and neuroplasticity. One “reader” of DNA methylation in particular, methyl-CpG-binding protein 2 (MeCP2), is highlighted, given its undisputed importance in neuronal function.
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47
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Demion M, Oger C, Vigor C, Thireau J, Guennec JYL, Durand T, Galano JM, Lee JCY. Two sides of the same coin: NEO-PUFAs in Rett syndrome and post-infarction cardiac arrhythmias. EUR J LIPID SCI TECH 2017. [DOI: 10.1002/ejlt.201600320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marie Demion
- Inserm U1046-UMR CNRS 9214 Physiologie et Médecine Expérimentale du cœur et des muscles−PHYMEDEX; Université de Montpellier; Montpellier France
| | - Camille Oger
- Institut des Biomolécules Max Mousseron, (IBMM) UMR 5247; CNRS Université de Montpellier, ENSCM; Montpellier France
| | - Claire Vigor
- Institut des Biomolécules Max Mousseron, (IBMM) UMR 5247; CNRS Université de Montpellier, ENSCM; Montpellier France
| | - Jérôme Thireau
- Inserm U1046-UMR CNRS 9214 Physiologie et Médecine Expérimentale du cœur et des muscles−PHYMEDEX; Université de Montpellier; Montpellier France
| | - Jean-Yves Le Guennec
- Inserm U1046-UMR CNRS 9214 Physiologie et Médecine Expérimentale du cœur et des muscles−PHYMEDEX; Université de Montpellier; Montpellier France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron, (IBMM) UMR 5247; CNRS Université de Montpellier, ENSCM; Montpellier France
| | - Jean-Marie Galano
- Institut des Biomolécules Max Mousseron, (IBMM) UMR 5247; CNRS Université de Montpellier, ENSCM; Montpellier France
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48
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Shulyakova N, Andreazza AC, Mills LR, Eubanks JH. Mitochondrial Dysfunction in the Pathogenesis of Rett Syndrome: Implications for Mitochondria-Targeted Therapies. Front Cell Neurosci 2017; 11:58. [PMID: 28352216 PMCID: PMC5348512 DOI: 10.3389/fncel.2017.00058] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/20/2017] [Indexed: 01/20/2023] Open
Abstract
First described over 50 years ago, Rett syndrome (RTT) is a neurodevelopmental disorder caused primarily by mutations of the X-linked MECP2 gene. RTT affects predominantly females, and has a prevalence of roughly 1 in every 10,000 female births. Prior to the discovery that mutations of MECP2 are the leading cause of RTT, there were suggestions that RTT could be a mitochondrial disease. In fact, several reports documented altered mitochondrial structure, and deficiencies in mitochondrial enzyme activity in different cells or tissues derived from RTT patients. With the identification of MECP2 as the causal gene, interest largely shifted toward defining the normal function of MeCP2 in the brain, and how its absence affects the neurodevelopment and neurophysiology. Recently, though, interest in studying mitochondrial function in RTT has been reignited, at least in part due to observations suggesting systemic oxidative stress does play a contributing role in RTT pathogenesis. Here we review data relating to mitochondrial alterations at the structural and functional levels in RTT patients and model systems, and present a hypothesis for how the absence of MeCP2 could lead to altered mitochondrial function and elevated levels of cellular oxidative stress. Finally, we discuss the prospects for treating RTT using interventions that target specific aspects of mitochondrial dysfunction and/or oxidative stress.
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Affiliation(s)
- Natalya Shulyakova
- Division of Genetics and Development, Krembil Research Institute, University Health NetworkToronto, ON, Canada; Department of Physiology, University of TorontoToronto, ON, Canada
| | - Ana C Andreazza
- Department of Pharmacology, University of Toronto Toronto, ON, Canada
| | - Linda R Mills
- Department of Physiology, University of Toronto Toronto, ON, Canada
| | - James H Eubanks
- Division of Genetics and Development, Krembil Research Institute, University Health NetworkToronto, ON, Canada; Department of Physiology, University of TorontoToronto, ON, Canada; Institute of Medical Sciences, University of TorontoToronto, ON, Canada; Department of Surgery (Neurosurgery), University of TorontoToronto, ON, Canada
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49
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Hu T, Zhu X, Pi W, Yu M, Shi H, Tuan D. Hypermethylated LTR retrotransposon exhibits enhancer activity. Epigenetics 2017; 12:226-237. [PMID: 28165867 DOI: 10.1080/15592294.2017.1289300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
LTR retrotransposons are repetitive DNA elements comprising ∼10% of the human genome. They are silenced by hypermethylation of cytosines in CpG dinucleotides and are considered parasitic DNA serving no useful function for the host genome. However, hypermethylated LTRs contain enhancer and promoter sequences and can promote tissue-specific transcription of cis-linked genes. To resolve the apparent paradox of hypermethylated LTRs possessing transcriptional activities, we studied the ERV-9 LTR retrotransposon located at the 5' border of the transcriptionally active β-globin gene locus in human erythroid progenitor and erythroleukemia K562 cells. We found that the ERV-9 LTR, containing 65 CpGs in 1.7 kb DNA, was hypermethylated (with > 90% methylated CpGs). Hypermethylated LTR possessed transcriptional enhancer activity, since in vivo deletion of the LTR by CRISPR-cas9 suppressed transcription of the globin genes by > 50%. ChIP-qPCR and ChIP-seq studies showed that the hypermethylated LTR enhancer spanning recurrent CCAATCG and GATA motifs associated respectively with key transcription factors (TFs) NF-Y and GATA-1 and -2 at reduced levels, compared with the unmethylated LTR in transfected LTR-reporter gene plasmids. Electrophoretic mobility shift assays with methylated LTR enhancer probe showed that the methylated probe bound both NF-Y and GATA-1 and -2 with lower affinities than the unmethylated enhancer probe. Thus, hypermethylation drastically reduced, but did not totally abolish, the binding affinities of the enhancer motifs to the key TFs to assemble the LTR-pol II transcription complex that activated transcription of cis-linked genes at reduced efficiency.
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Affiliation(s)
- Tianxiang Hu
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Xingguo Zhu
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Wenhu Pi
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Miao Yu
- b Georgia Cancer Center , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Huidong Shi
- b Georgia Cancer Center , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Dorothy Tuan
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
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50
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Claveria-Gimeno R, Lanuza PM, Morales-Chueca I, Jorge-Torres OC, Vega S, Abian O, Esteller M, Velazquez-Campoy A. The intervening domain from MeCP2 enhances the DNA affinity of the methyl binding domain and provides an independent DNA interaction site. Sci Rep 2017; 7:41635. [PMID: 28139759 PMCID: PMC5282554 DOI: 10.1038/srep41635] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/22/2016] [Indexed: 01/09/2023] Open
Abstract
Methyl-CpG binding protein 2 (MeCP2) preferentially interacts with methylated DNA and it is involved in epigenetic regulation and chromatin remodelling. Mutations in MeCP2 are linked to Rett syndrome, the leading cause of intellectual retardation in girls and causing mental, motor and growth impairment. Unstructured regions in MeCP2 provide the plasticity for establishing interactions with multiple binding partners. We present a biophysical characterization of the methyl binding domain (MBD) from MeCP2 reporting the contribution of flanking domains to its structural stability and dsDNA interaction. The flanking disordered intervening domain (ID) increased the structural stability of MBD, modified its dsDNA binding profile from an entropically-driven moderate-affinity binding to an overwhelmingly enthalpically-driven high-affinity binding. Additionally, ID provided an additional site for simultaneously and autonomously binding an independent dsDNA molecule, which is a key feature linked to the chromatin remodelling and looping activity of MeCP2, as well as its ability to interact with nucleosomes replacing histone H1. The dsDNA interaction is characterized by an unusually large heat capacity linked to a cluster of water molecules trapped within the binding interface. The dynamics of disordered regions together with extrinsic factors are key determinants of MeCP2 global structural properties and functional capabilities.
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Affiliation(s)
- Rafael Claveria-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, 50018, Spain.,Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, 50009, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, 50009, Spain
| | - Pilar M Lanuza
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, 50018, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, 50009, Spain.,Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, 50009, Spain
| | - Ignacio Morales-Chueca
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, 50018, Spain.,Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, 50009, Spain
| | - Olga C Jorge-Torres
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, 08908, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, 50018, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, 50018, Spain.,Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, 50009, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, 50009, Spain.,Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, 50009, Spain.,Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, 08908, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, L'Hospitalet de Llobregat, Barcelona, 08907, Spain.,Institucio Catalana de Recerca i Estudis Avançats, Barcelona, 08010, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, 50018, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, 50009, Spain.,Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, 50009, Spain.,Fundacion ARAID, Government of Aragon, Zaragoza, 50018, Spain
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